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rpob

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This commit is contained in:
Tanushree Tunstall 2022-08-29 18:23:43 +01:00
parent 6441be21ab
commit 8f97ab7cc8
4 changed files with 17 additions and 15 deletions
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4
config/rpob.R
View file

@ -65,8 +65,8 @@ cat("\n==================================================="
aa_pos_lig1 = NULL
aa_pos_lig2 = NULL
aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("RPO","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple"))
tile_map=data.frame(tile=c("RFP"),
tile_colour=c("green"))
####

1
scripts/functions/bp_lineage.R
View file

@ -29,6 +29,7 @@ lin_count_bp <- function( lf_data = lin_lf
, y_log10 = FALSE
, y_scale_percent = FALSE
, y_label = c("Count", "SNP diversity")
, ...
#, y_label = c("Count")
) {
if(!all_lineages){

2
scripts/functions/bp_lineage_diversity.R
View file

@ -36,7 +36,7 @@ lin_count_bp_diversity <- function( lf_data = lin_wf
, subtitle_text = NULL
, sts = 20
, subtitle_colour = "#350E20FF" #brown
) {
, ...) {
if(!all_lineages){
lf_data = lf_data[lf_data[[x_categ]]%in%use_lineages,]
}

25
scripts/functions/logoP_or.R
View file

@ -79,11 +79,12 @@ LogoPlotCustomH <- function(plot_df
#-------------------
if (y_axis_log){
log_colname = paste0("log_", y_axis_colname)
plot_df[log_colname] = log_value(plot_df[y_axis_colname])
log_colname = paste0("log10_", y_axis_colname)
#plot_df[log_colname] = log_value(plot_df[y_axis_colname])
#plot_df[[log_colname]] = log10(plot_df[y_axis_colname])
logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
logo_df_plot = logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)
logo_df_plot = logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0)
rownames(logo_df_plot) = logo_df_plot$mutant_type
logo_df_plot$mutant_type = NULL
logo_dfP_wf=as.matrix(logo_df_plot)
@ -151,15 +152,15 @@ LogoPlotCustomH <- function(plot_df
ytt_col = "black"
}
if (y_axis_log){
if (grepl("Log", y_lab)){
y_lab = y_lab
}else{
y_lab = paste("Log", y_lab)
}
}
# if (y_axis_log){
#
# if (grepl("Log", y_lab)){
# y_lab = y_lab
#
# }else{
# y_lab = paste("Log", y_lab)
# }
# }
plot_grid(
ggplot() +
geom_logo(logo_dfP_wf